Two years after the world as we know it has ended, Shizuru leads an uneventful life in her hometown of Agano. But one day, she finds a clue that will lead her on a journey into the unknown to find her missing friend.

Shizuru and the others depart on their journey to Ikebukuro, but find that they are woefully lacking in supplies. As they ride along the Koma River, they spot a mysterious, long-necked shadow.

The gang finds themselves welcomed by the friendly townsfolk of Higashi-Agano. Akira, however, can't shake the feeling that all is not as it seems with their generous hosts.

As the train continues on its journey to Ikebukuro, each new stop begins to take weirder, wilder turns. Meanwhile, Akira appears to be hiding something from the others.

Shizuru and Reimi find themselves prisoners near Inariyama Park. They must escape their tiny captors, and find a doctor to cure Akira's affliction before it's too late.

Pochi-san appears to be feeling sick, much to Akira's dismay. In the ensuing argument, Nadeshiko confronts Shizuru to find out the truth about why Yoka has gone missing.